Mercurial > repos > s-kaufmann > synteny_mapper

changeset 18:cc66a156025d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 10:50:34 -0400
parents 98c0153c737a
children 6cbc54be9466
files tool_dependencies.xml visualization.xml
diffstat 2 files changed, 3 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 15 10:31:26 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 10:50:34 2014 -0400
@@ -31,48 +31,7 @@
 	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 
-     <package name="readline" version="6.2">
-        <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ncurses" version="5.9">
-        <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="libpng" version="1.6.7">
-        <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+     <package name="package_r_3_0_2" version="3.0.2">
+        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="R_3_0_2" version="3.0.2">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="readline" version="6.2" />
-                    </repository>
-                    <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="ncurses" version="5.9" />
-                    </repository>
-                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="libpng" version="1.6.7" />
-                    </repository>
-</action>
-
-                <action type="shell_command">
-                    ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
-                </action>
-
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
-    </package>
-
 </tool_dependency>
--- a/visualization.xml	Fri Aug 15 10:31:26 2014 -0400
+++ b/visualization.xml	Fri Aug 15 10:50:34 2014 -0400
@@ -5,7 +5,7 @@
     <requirement type="set_environment">JAR_PATH</requirement>
     <requirement type="package" version="0.64">circos</requirement>
     <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
-    <requirement type="package" version="3.0.2">R_3_0_2</requirement>
+    <requirement type="package" version="3.0.2">package_r_3_0_2</requirement>
     <requirement type="set_environment">R_PATH</requirement>
 </requirements>